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fix wrong assumption to file start
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Co-authored-by: Alex Aperis <[email protected]>
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blankdots and aaperis committed Jan 16, 2024
1 parent 7b8771e commit 6810871
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Showing 5 changed files with 52 additions and 14 deletions.
6 changes: 4 additions & 2 deletions .github/integration/tests/common/50_check_endpoint.sh
Original file line number Diff line number Diff line change
Expand Up @@ -92,26 +92,28 @@ fi

curl --cacert certs/ca.pem -H "Authorization: Bearer $token" "https://localhost:8443/files/urn:neic:001-002?startCoordinate=0&endCoordinate=2" --output test-part.txt

echo "TH" > old-part.txt
dd if=old-file.txt ibs=1 skip=0 count=2 > old-part.txt

cmp --silent old-part.txt test-part.txt
status=$?
if [[ $status = 0 ]]; then
echo "Files are the same"
else
echo "Files are different"
exit 1
fi

curl --cacert certs/ca.pem -H "Authorization: Bearer $token" "https://localhost:8443/files/urn:neic:001-002?startCoordinate=7&endCoordinate=14" --output test-part2.txt

echo "LE IS J" > old-part2.txt
dd if=old-file.txt ibs=1 skip=7 count=7 > old-part2.txt

cmp --silent old-part2.txt test-part2.txt
status=$?
if [[ $status = 0 ]]; then
echo "Files are the same"
else
echo "Files are different"
exit 1
fi

# ------------------
Expand Down
6 changes: 4 additions & 2 deletions .github/integration/tests/s3notls/52_check_endpoint.sh
Original file line number Diff line number Diff line change
Expand Up @@ -88,26 +88,28 @@ fi

curl -H "Authorization: Bearer $token" "http://localhost:8080/files/urn:neic:001-002?startCoordinate=0&endCoordinate=2" --output test-part.txt

echo "TH" > old-part.txt
dd if=old-file.txt ibs=1 skip=0 count=2 > old-part.txt

cmp --silent old-part.txt test-part.txt
status=$?
if [[ $status = 0 ]]; then
echo "Files are the same"
else
echo "Files are different"
exit 1
fi

curl -H "Authorization: Bearer $token" "http://localhost:8080/files/urn:neic:001-002?startCoordinate=7&endCoordinate=14" --output test-part2.txt

echo "LE IS J" > old-part2.txt
dd if=old-file.txt ibs=1 skip=7 count=7 > old-part2.txt

cmp --silent old-part2.txt test-part2.txt
status=$?
if [[ $status = 0 ]]; then
echo "Files are the same"
else
echo "Files are different"
exit 1
fi

# ------------------
Expand Down
7 changes: 7 additions & 0 deletions api/sda/sda.go
Original file line number Diff line number Diff line change
Expand Up @@ -255,6 +255,13 @@ func Download(c *gin.Context) {
// used from: https://github.com/neicnordic/crypt4gh/blob/master/examples/reader/main.go#L48C1-L113C1
var sendStream = func(reader *streaming.Crypt4GHReader, writer http.ResponseWriter, start, end int64) error {

if start != 0 {
// We don't want to read from start, skip ahead to where we should be
if _, err := reader.Seek(start, 0); err != nil {
return err
}
}

// Calculate how much we should read (if given)
togo := end - start

Expand Down
2 changes: 1 addition & 1 deletion go.mod
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ require (
github.com/dgraph-io/ristretto v0.1.1
github.com/gin-gonic/gin v1.9.1
github.com/google/uuid v1.5.0
github.com/johannesboyne/gofakes3 v0.0.0-20230129080941-f6a8a9ae6fd3
github.com/johannesboyne/gofakes3 v0.0.0-20230914150226-f005f5cc03aa
github.com/lestrrat-go/jwx/v2 v2.0.19
github.com/lib/pq v1.10.9
github.com/neicnordic/crypt4gh v1.8.8
Expand Down
45 changes: 36 additions & 9 deletions go.sum
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ filippo.io/edwards25519 v1.1.0 h1:FNf4tywRC1HmFuKW5xopWpigGjJKiJSV0Cqo0cJWDaA=
filippo.io/edwards25519 v1.1.0/go.mod h1:BxyFTGdWcka3PhytdK4V28tE5sGfRvvvRV7EaN4VDT4=
github.com/DATA-DOG/go-sqlmock v1.5.2 h1:OcvFkGmslmlZibjAjaHm3L//6LiuBgolP7OputlJIzU=
github.com/DATA-DOG/go-sqlmock v1.5.2/go.mod h1:88MAG/4G7SMwSE3CeA0ZKzrT5CiOU3OJ+JlNzwDqpNU=
github.com/aws/aws-sdk-go v1.33.0/go.mod h1:5zCpMtNQVjRREroY7sYe8lOMRSxkhG6MZveU8YkpAk0=
github.com/aws/aws-sdk-go v1.44.256/go.mod h1:aVsgQcEevwlmQ7qHE9I3h+dtQgpqhFB+i8Phjh7fkwI=
github.com/aws/aws-sdk-go v1.49.21 h1:Rl8KW6HqkwzhATwvXhyr7vD4JFUMi7oXGAw9SrxxIFY=
github.com/aws/aws-sdk-go v1.49.21/go.mod h1:LF8svs817+Nz+DmiMQKTO3ubZ/6IaTpq3TjupRn3Eqk=
github.com/bytedance/sonic v1.5.0/go.mod h1:ED5hyg4y6t3/9Ku1R6dU/4KyJ48DZ4jPhfY1O2AihPM=
Expand Down Expand Up @@ -49,7 +49,6 @@ github.com/go-playground/universal-translator v0.18.1 h1:Bcnm0ZwsGyWbCzImXv+pAJn
github.com/go-playground/universal-translator v0.18.1/go.mod h1:xekY+UJKNuX9WP91TpwSH2VMlDf28Uj24BCp08ZFTUY=
github.com/go-playground/validator/v10 v10.15.2 h1:Ra5cll2/eF8X0Ff2+8SMD7euo2nenQ8WEpgqfy4NhHU=
github.com/go-playground/validator/v10 v10.15.2/go.mod h1:9iXMNT7sEkjXb0I+enO7QXmzG6QCsPWY4zveKFVRSyU=
github.com/go-sql-driver/mysql v1.5.0/go.mod h1:DCzpHaOWr8IXmIStZouvnhqoel9Qv2LBy8hT2VhHyBg=
github.com/goccy/go-json v0.10.2 h1:CrxCmQqYDkv1z7lO7Wbh2HN93uovUHgrECaO5ZrCXAU=
github.com/goccy/go-json v0.10.2/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I=
github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q=
Expand All @@ -63,13 +62,12 @@ github.com/google/uuid v1.5.0 h1:1p67kYwdtXjb0gL0BPiP1Av9wiZPo5A8z2cWkTZ+eyU=
github.com/google/uuid v1.5.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
github.com/hashicorp/hcl v1.0.0 h1:0Anlzjpi4vEasTeNFn2mLJgTSwt0+6sfsiTG8qcWGx4=
github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ=
github.com/jmespath/go-jmespath v0.3.0/go.mod h1:9QtRXoHjLGCJ5IBSaohpXITPlowMeeYCZ7fLUTSywik=
github.com/jmespath/go-jmespath v0.4.0 h1:BEgLn5cpjn8UN1mAw4NjwDrS35OdebyEtFe+9YPoQUg=
github.com/jmespath/go-jmespath v0.4.0/go.mod h1:T8mJZnbsbmF+m6zOOFylbeCJqk5+pHWvzYPziyZiYoo=
github.com/jmespath/go-jmespath/internal/testify v1.5.1 h1:shLQSRRSCCPj3f2gpwzGwWFoC7ycTf1rcQZHOlsJ6N8=
github.com/jmespath/go-jmespath/internal/testify v1.5.1/go.mod h1:L3OGu8Wl2/fWfCI6z80xFu9LTZmf1ZRjMHUOPmWr69U=
github.com/johannesboyne/gofakes3 v0.0.0-20230129080941-f6a8a9ae6fd3 h1:aTscQmvmU/1AS3PqVaNtUtJUwyMexxqVErkhwsWoEpw=
github.com/johannesboyne/gofakes3 v0.0.0-20230129080941-f6a8a9ae6fd3/go.mod h1:Cnosl0cRZIfKjTMuH49sQog2LeNsU5Hf4WnPIDWIDV0=
github.com/johannesboyne/gofakes3 v0.0.0-20230914150226-f005f5cc03aa h1:a6Hc6Hlq6MxPNBW53/S/HnVwVXKc0nbdD/vgnQYuxG0=
github.com/johannesboyne/gofakes3 v0.0.0-20230914150226-f005f5cc03aa/go.mod h1:AxgWC4DDX54O2WDoQO1Ceabtn6IbktjU/7bigor+66g=
github.com/json-iterator/go v1.1.12 h1:PV8peI4a0ysnczrg+LtxykD8LfKY9ML6u2jnxaEnrnM=
github.com/json-iterator/go v1.1.12/go.mod h1:e30LSqwooZae/UwlEbR2852Gd8hjQvJoHmT4TnhNGBo=
github.com/kisielk/sqlstruct v0.0.0-20201105191214-5f3e10d3ab46/go.mod h1:yyMNCyc/Ib3bDTKd379tNMpB/7/H5TjM2Y9QJ5THLbE=
Expand Down Expand Up @@ -124,7 +122,6 @@ github.com/sagikazarmark/slog-shim v0.1.0 h1:diDBnUNK9N/354PgrxMywXnAwEr1QZcOr6g
github.com/sagikazarmark/slog-shim v0.1.0/go.mod h1:SrcSrq8aKtyuqEI1uvTDTK1arOWRIczQRv+GVI1AkeQ=
github.com/segmentio/asm v1.2.0 h1:9BQrFxC+YOHJlTlHGkTrFWf59nbL3XnCoFLTwDCI7ys=
github.com/segmentio/asm v1.2.0/go.mod h1:BqMnlJP91P8d+4ibuonYZw9mfnzI9HfxselHZr5aAcs=
github.com/shabbyrobe/gocovmerge v0.0.0-20180507124511-f6ea450bfb63/go.mod h1:n+VKSARF5y/tS9XFSP7vWDfS+GUC5vs/YT7M5XDTUEM=
github.com/shabbyrobe/gocovmerge v0.0.0-20190829150210-3e036491d500 h1:WnNuhiq+FOY3jNj6JXFT+eLN3CQ/oPIsDPRanvwsmbI=
github.com/shabbyrobe/gocovmerge v0.0.0-20190829150210-3e036491d500/go.mod h1:+njLrG5wSeoG4Ds61rFgEzKvenR2UHbjMoDHsczxly0=
github.com/sirupsen/logrus v1.9.3 h1:dueUQJ1C2q9oE3F7wvmSGAaVtTmUizReu6fjN8uqzbQ=
Expand Down Expand Up @@ -160,6 +157,7 @@ github.com/twitchyliquid64/golang-asm v0.15.1 h1:SU5vSMR7hnwNxj24w34ZyCi/FmDZTkS
github.com/twitchyliquid64/golang-asm v0.15.1/go.mod h1:a1lVb/DtPvCB8fslRZhAngC2+aY1QWCk3Cedj/Gdt08=
github.com/ugorji/go/codec v1.2.11 h1:BMaWp1Bb6fHwEtbplGBGJ498wD+LKlNSl25MjdZY4dU=
github.com/ugorji/go/codec v1.2.11/go.mod h1:UNopzCgEMSXjBc6AOMqYvWC1ktqTAfzJZUZgYf6w6lg=
github.com/yuin/goldmark v1.4.13/go.mod h1:6yULJ656Px+3vBD8DxQVa3kxgyrAnzto9xy5taEt/CY=
go.etcd.io/bbolt v1.3.5/go.mod h1:G5EMThwa9y8QZGBClrRx5EY+Yw9kAhnjy3bSjsnlVTQ=
go.uber.org/atomic v1.9.0 h1:ECmE8Bn/WFTYwEW/bpKD3M8VtR/zQVbavAoalC1PYyE=
go.uber.org/atomic v1.9.0/go.mod h1:fEN4uk6kAWBTFdckzkM89CLk9XfWZrxpCo0nPH17wJc=
Expand All @@ -169,30 +167,59 @@ golang.org/x/arch v0.0.0-20210923205945-b76863e36670/go.mod h1:5om86z9Hs0C8fWVUu
golang.org/x/arch v0.4.0 h1:A8WCeEWhLwPBKNbFi5Wv5UTCBx5zzubnXDlMOFAzFMc=
golang.org/x/arch v0.4.0/go.mod h1:5om86z9Hs0C8fWVUuoMHwpExlXzs5Tkyp9hOrfG7pp8=
golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
golang.org/x/crypto v0.17.0 h1:r8bRNjWL3GshPW3gkd+RpvzWrZAwPS49OmTGZ/uhM4k=
golang.org/x/crypto v0.17.0/go.mod h1:gCAAfMLgwOJRpTjQ2zCCt2OcSfYMTeZVSRtQlPC7Nq4=
golang.org/x/exp v0.0.0-20240110193028-0dcbfd608b1e h1:723BNChdd0c2Wk6WOE320qGBiPtYx0F0Bbm1kriShfE=
golang.org/x/exp v0.0.0-20240110193028-0dcbfd608b1e/go.mod h1:iRJReGqOEeBhDZGkGbynYwcHlctCvnjTYIamk7uXpHI=
golang.org/x/net v0.0.0-20190213061140-3a22650c66bd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4=
golang.org/x/mod v0.8.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
golang.org/x/mod v0.10.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20200202094626-16171245cfb2/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
golang.org/x/net v0.0.0-20210226172049-e18ecbb05110/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg=
golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c=
golang.org/x/net v0.1.0/go.mod h1:Cx3nUiGt4eDBEyega/BKRp+/AlGL8hYe7U9odMt2Cco=
golang.org/x/net v0.6.0/go.mod h1:2Tu9+aMcznHK/AK1HMvgo6xiTLG5rD5rZLDS+rp2Bjs=
golang.org/x/net v0.9.0/go.mod h1:d48xBJpPfHeWQsugry2m+kC02ZBRGRgulfHnEXEuWns=
golang.org/x/net v0.19.0 h1:zTwKpTd2XuCqf8huc7Fo2iSy+4RHPd10s4KzeTnVr1c=
golang.org/x/net v0.19.0/go.mod h1:CfAk/cbD4CthTvqiEl8NpboMuiuOYsAr/7NOjZJtv1U=
golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
golang.org/x/sync v0.1.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
golang.org/x/sys v0.0.0-20200202164722-d101bd2416d5/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20220520151302-bc2c85ada10a/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20221010170243-090e33056c14/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.1.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.5.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.7.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.16.0 h1:xWw16ngr6ZMtmxDyKyIgsE93KNKz5HKmMa3b8ALHidU=
golang.org/x/sys v0.16.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
golang.org/x/term v0.1.0/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
golang.org/x/term v0.5.0/go.mod h1:jMB1sMXY+tzblOD4FWmEbocvup2/aLOaQEp7JmGp78k=
golang.org/x/term v0.7.0/go.mod h1:P32HKFT3hSsZrRxla30E9HqToFYAQPCMs/zFMBUFqPY=
golang.org/x/term v0.16.0 h1:m+B6fahuftsE9qjo0VWp2FW0mB3MTJvR0BaMQrq0pmE=
golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ=
golang.org/x/text v0.4.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
golang.org/x/text v0.7.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
golang.org/x/text v0.9.0/go.mod h1:e1OnstbJyHTd6l/uOt8jFFHp6TRDWZR/bV3emEE/zU8=
golang.org/x/text v0.14.0 h1:ScX5w1eTa3QqT8oi6+ziP7dTV1S2+ALU0bI+0zXKWiQ=
golang.org/x/text v0.14.0/go.mod h1:18ZOQIKpY8NJVqYksKHtTdi31H5itFRjB5/qKTNYzSU=
golang.org/x/tools v0.0.0-20190308174544-00c44ba9c14f/go.mod h1:25r3+/G6/xytQM8iWZKq3Hn0kr0rgFKPUNVEL/dr3z4=
golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
golang.org/x/tools v0.0.0-20190829051458-42f498d34c4d/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc=
golang.org/x/tools v0.6.0/go.mod h1:Xwgl3UAJ/d3gWutnCtw505GrjyAbvKui8lOU390QaIU=
golang.org/x/tools v0.8.0/go.mod h1:JxBZ99ISMI5ViVkT1tr6tdNmXeTrcpVSD3vZ1RsRdN4=
golang.org/x/tools v0.16.0 h1:GO788SKMRunPIBCXiQyo2AaexLstOrVhuAL5YwsckQM=
golang.org/x/tools v0.16.0/go.mod h1:kYVVN6I1mBNoB1OX+noeBjbRk4IUEPa7JJ+TJMEooJ0=
golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
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